The Gulf of California (GC) is the only interior sea in the Eastern Pacific Ocean and is the most important fishing area in the northwestern region of the Mexican Pacific. This study focuses on the oceanographic variability of the GC, including its southern portion, which is an area with a high flow of energy and exchange of properties with the Pacific Ocean (PO), in order to determine its role in physical–biological cycles and climate change. The purpose of this work is to analyze the sea surface temperature (SST) and chlorophyll a concentration (Chl-a) during the period from 1998–2022 as indicators of long-term physical and biological processes, oceanographic variability, and primary production in the GC. In total, 513 subareas in the GC were analyzed, and a cluster analysis was applied to identify similar areas in terms of SST and Chl-a via the K-means method and using the silhouette coefficient (>0.5) as a metric to validate the clusters obtained. The trends of the time series of both variables were analyzed, and a fast Fourier analysis was performed to evaluate cycles in the series. A descriptive analysis of the SST and Chl-a series showed that the SST decreased from south to north. Six bioregions were identified using a combined of both SST and Chl-a data. The spectral analysis of the SST showed that the main frequencies in the six bioregions were annual and interannual (3–7 years), and the frequencies of their variations were associated with basin-level weather events, such as El Niño and La Niña. The SST in the GC showed a heating trend at an annual rate of ~0.036 °C (~0.73 °C in 20 years) and a decrease in Chl-a at an annual rate of ~0.012 mg/m³ (~0.25 mg/m³ in 20 years), with potential consequences for communities and ecosystems. Additionally, cycles of 10–13 and 15–20 years were identified, and the 10–13-year cycle explained almost 40–50% of the signal power in some regions. Moreover, mesoscale features (eddies and filaments) were identified along the GC, and they were mainly associated with the clusters of the SST. All these spatial and temporal variabilities induce conditions that generate different habitats and could explain the high biodiversity of the GC. If the warming trend of the SST and the decreasing trend of the Chl-a continue in the long term, concerns could be raised, as they can have important effects on the dynamics of this important marine ecosystem, including habitat loss for numerous native species, declines in the catches of the main fishery resources, and, consequently, support for the arrival of harmful invasive species.

Oceanic mesoscale events such as eddies, coastal upwelling, filaments and fronts created by water mass intrusion present properties allowing them to concentrate, transport and disperse salt, nutrients and plankton, among other important constituents in the ocean. The use of satellite images enables the continuous monitoring of the ocean dynamics at different temporal and spatial scales, aiding the study of its variability. This study focuses on the identification of these mesoscale events in the Gulf of California (GC) by means of sea surface temperature (SST) and chlorophyll a (Chl a) fronts (edge) detection by processing 5-day satellite images from the 1998–2019 period. The annual occurrence or frequency and duration of each event was identified; the interannual variability was evaluated and underlying correlations with the Multivariate El Niño Index (MEI) and the Pacific Decadal Index (PDOI) were assessed via Principal Component Analysis. Most events showed a seasonal variability due to the seasonal behavior of forcing agents (i.e., Pacific Ocean and winds) that stimulate their formation or presence in the GC; seasonality was more evident in the northern region than in the southern region. The interannual variability of their frequency or duration was associated with strong and intense El Niño and La Niña conditions (positive or negative MEI values) together with positive or negative phases of the PDOI. The use of SST and Chl a satellite images with a 5-day temporal resolution allowed to better identify and quantify the annual frequency and duration of each mesoscale event. It allowed to detect a seasonal behavior of these events in the northern region, followed by the central region. The southern region, due to the interaction of different water masses with unique characteristics, exhibited a less evident seasonality in the frequency of eddies, and no apparent association between their interannual frequency and duration with the MEI and PDOI. Constantly monitoring these oceanic events and their variability will help in the understanding of how the different regions of this large marine ecosystem respond to these variations in the long term.